Fig 1.
Time-course fermentation profile.
Fermentation profile of E. coli K-12 MG1655 growing in a minimal glucose medium before sampling of biomass at ∼7.5 h. (A) Glucose concentration [mM], CO2 in the off-gas [mmol h−1], respiratory quotient (RQ) [unitless], and OD600 [unitless]. Unity is highlighted on the same axis as the RQ for reference. The final OD600 was estimated from the measured cell concentration of 2.6 gCDW L−1 at sampling, assuming a cell dry weight to OD600 conversion factor of 0.5 [15, 48]. (B) Concentrations [mM] of the fermentation products lactate, formate, acetate, and succinate. The same figure, except plotted from t = 0, can be seen in S4 Fig.
Table 1.
Macromolecular biomass composition.
Overview of the average mass fractions [g gCDW−1] for the experimentally measured biomass components of E. coli K-12 MG1655. Also presented are the previously published E. coli biomass compositions by Neidhardt [38] and Beck et al. [15]. Standard deviations are included in parentheses. Abbreviations: NA for not applicable, n.d. for not detected,—for not measured/reported, KDO for 2-keto-3-deoxy-octonate.
Fig 2.
Adjustments of BOF stoichiometries impact attainable flux ranges.
(A) Rank-ordered, relative value of BOF coefficients, Sr (Eq 2), of eBOF compared to mBOF. (B) Histogram of fractional overlap of attainable flux ranges, ξ (Eq 1), for all model reactions using mBOF versus eBOF.
Table 2.
Significant changes in attainable flux ranges.
Examples of reactions in iML1515 with a significant shift in feasible flux range when using eBOF. The flux ranges for mBOF is also presented, as well as the relative change in center point (CPr) of the corresponding flux ranges. Abbreviations: MCOATA for malonyl-CoA-ACP transacylase, UAGDP for UDP-N-acetylglucosamine diphosphorylase, POR5 for pyruvate synthase, TMDS for thymidylate synthase.